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annotate vpt_segment.xml @ 2:a88a1e78702e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
author bgruening
date Sun, 22 Jun 2025 12:25:48 +0000
parents ed28a1feba82
children 0811613196a2
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5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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1 <tool id="vpt_segment" name="Vizgen VPT - Segment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>cells and refine MERSCOPE experiments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="creator" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @CMD@
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10 ln -s '$detected_transcripts' 'input/detected_transcripts.csv' &&
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11 ln -s '$vpt_config_file' 'input/vpt_config_file.json' &&
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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12 ### segmentation
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13 vpt
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14 @COMMON_ARGS@
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15 run-segmentation
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16 --segmentation-algorithm 'input/vpt_config_file.json'
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17 --input-images 'input/images/'
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18 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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19 --output-path 'output/'
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20 --tile-size $tile_size
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21 #if $max_row_group_size:
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22 --max-row-group-size $max_row_group_size
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23 #end if
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24 --tile-overlap $tile_overlap &&
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25 ### counting partition transcripts
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26 vpt
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27 @COMMON_ARGS@
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28 partition-transcripts
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29 --input-boundaries 'output/cellpose2_micron_space.parquet'
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30 --input-transcripts 'input/detected_transcripts.csv'
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31 --output-entity-by-gene 'output/cell_by_gene.csv'
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32 --output-transcripts 'output/detected_transcripts.csv' &&
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33 ### sum signals
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34 vpt
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35 @COMMON_ARGS@
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36 sum-signals
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37 --input-images 'input/images/'
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38 --input-boundaries 'output/cellpose2_micron_space.parquet'
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39 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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40 --output-csv 'output/sum_signals.csv' &&
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41 ### derive entity metadata
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42 vpt
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43 @COMMON_ARGS@
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44 derive-entity-metadata
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45 --input-boundaries 'output/cellpose2_micron_space.parquet'
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46 --input-entity-by-gene 'output/cell_by_gene.csv'
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47 --output-metadata 'output/cell_metadata.csv' &&
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48 ### segmentation QC
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49 vpt
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50 @COMMON_ARGS@
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51 generate-segmentation-metrics
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52 --input-entity-by-gene 'output/cell_by_gene.csv'
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53 --input-metadata 'output/cell_metadata.csv'
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54 --input-transcripts 'output/detected_transcripts.csv'
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55 --input-boundaries 'output/cellpose2_micron_space.parquet'
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56 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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57 --input-images 'input/images/'
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58 --experiment-name '$qc_params.experiment_name'
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59 --input-z-index '$qc_params.input_z_index'
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60 #if $qc_params.red_stain_name != "None":
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61 --red-stain-name '$qc_params.red_stain_name'
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62 #end if
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63 #if $qc_params.green_stain_name != "None":
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64 --green-stain-name '$qc_params.green_stain_name'
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65 #end if
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66 #if $qc_params.blue_stain_name != "None":
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67 --blue-stain-name '$qc_params.blue_stain_name'
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68 #end if
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69 --transcript-count-filter-threshold '$qc_params.transcript_count_filter_threshold'
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70 --volume-filter-threshold '$qc_params.volume_filter_threshold'
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71 --output-csv 'output/metrics.csv'
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72 --output-report 'output/metrics.html'
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73 --output-clustering 'output/metrics_clustering.parquet' &&
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74 mv 'input/vpt_config_file.json' 'output/vpt_config_file.json'
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75 ]]></command>
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76 <configfiles>
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77 <configfile name="vpt_config_file"><![CDATA[
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78 {
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79 "experiment_properties": {
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80 #set $indices = ",".join([str(i) for i in range(len(str($vpt_config.experiment_properties.z_positions_um.value).split(",")))])
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81
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82 "all_z_indexes": [$indices],
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83 "z_positions_um": [$vpt_config.experiment_properties.z_positions_um]
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84 },
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85 "segmentation_tasks": [
1
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86 #set $task_n = len($vpt_config.segmentation_tasks.segmentation_task) - 1
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87 #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
0
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88 {
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89 "task_id": $i,
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90 "segmentation_family": "Cellpose2",
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91 #if $task.entity_types_detected != "both":
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92 "entity_types_detected": ["$task.entity_types_detected"],
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93 #else:
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94 "entity_types_detected": [
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95 "nuclei",
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96 "cell"
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97 ],
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98 #end if
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99 "z_layers": [$task.z_layers],
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100 "segmentation_properties": {
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101 #if $task.segmentation_properties.model != "null":
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102 "model": "$task.segmentation_properties.model",
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103 #else:
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104 "model": null,
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105 #end if
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106 "model_dimensions": "$task.segmentation_properties.model_dimensions",
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107 #if $task.segmentation_properties.custom_weights:
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108 "custom_weights": "$task.segmentation_properties.custom_weights",
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109 #else:
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110 "custom_weights": null,
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111 #end if
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112 "channel_map": {
2
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113 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None":
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114 "red": "$task.segmentation_properties.channel_map.channel_red_conditional.red",
0
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115 #else:
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116 "red": "",
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117 #end if
2
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118 #if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None":
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119 "green": "$task.segmentation_properties.channel_map.channel_green_conditional.green",
0
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120 #else:
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121 "green": "",
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122 #end if
2
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123 #if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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124 "blue": "$task.segmentation_properties.channel_map.channel_blue_conditional.blue"
0
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125 #else:
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126 "blue": ""
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127 #end if
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128 }
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129 },
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130 "task_input_data": [
2
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131 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None":
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132 #set $input_data = $task.segmentation_properties.channel_map.channel_red_conditional
0
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133 {
2
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134 "image_channel": "$task.segmentation_properties.channel_map.channel_red_conditional.red",
0
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135 "image_preprocessing": [
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136 #if $input_data.normalize_conditional.normalize_select == "Yes":
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137 {
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138 "name": "normalize",
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139 "parameters": {
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140 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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141 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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142 "filter_size": [
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143 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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144 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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145 ],
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146 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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147 #end if
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148 }
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149 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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150 ,
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151 #end if
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152 #end if
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153 #if $input_data.blur_conditional.blur_select == "Yes":
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154 {
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155 "name": "blur",
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156 "parameters": {
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157 "type": "$input_data.blur_conditional.blur_options",
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158 "size": $input_data.blur_conditional.kernel_size
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159 }
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160 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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161 ,
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162 #end if
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163 #end if
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164 #if $input_data.downsample_conditional.downsample_select == "Yes":
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165 {
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166 "name": "downsample",
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167 "parameters": {
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168 "scale": "$input_data.downsample_conditional.scale"
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169 }
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170 }
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171 #end if
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172 ]
2
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173 }#if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None" or $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
0
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174 ,
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175 #end if
2
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176 #end if
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177 #if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None":
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178 #set $input_data = $task.segmentation_properties.channel_map.channel_green_conditional
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179 {
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180 "image_channel": "$task.segmentation_properties.channel_map.channel_green_conditional.green",
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181 "image_preprocessing": [
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182 #if $input_data.normalize_conditional.normalize_select == "Yes":
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183 {
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184 "name": "normalize",
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185 "parameters": {
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186 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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187 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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188 "filter_size": [
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189 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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190 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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191 ],
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192 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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193 #end if
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194 }
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195 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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196 ,
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197 #end if
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198 #end if
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199 #if $input_data.blur_conditional.blur_select == "Yes":
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200 {
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201 "name": "blur",
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202 "parameters": {
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203 "type": "$input_data.blur_conditional.blur_options",
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204 "size": $input_data.blur_conditional.kernel_size
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205 }
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206 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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207 ,
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208 #end if
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209 #end if
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210 #if $input_data.downsample_conditional.downsample_select == "Yes":
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211 {
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212 "name": "downsample",
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213 "parameters": {
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214 "scale": "$input_data.downsample_conditional.scale"
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215 }
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216 }
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217 #end if
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218 ]
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219 }#if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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220 ,
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221 #end if
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222 #end if
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223 #if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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224 #set $input_data = $task.segmentation_properties.channel_map.channel_blue_conditional
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225 {
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226 "image_channel": "$task.segmentation_properties.channel_map.channel_blue_conditional.blue",
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227 "image_preprocessing": [
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228 #if $input_data.normalize_conditional.normalize_select == "Yes":
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229 {
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230 "name": "normalize",
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231 "parameters": {
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232 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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233 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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234 "filter_size": [
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235 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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236 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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237 ],
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238 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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239 #end if
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240 }
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241 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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242 ,
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243 #end if
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244 #end if
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245 #if $input_data.blur_conditional.blur_select == "Yes":
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246 {
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247 "name": "blur",
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248 "parameters": {
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249 "type": "$input_data.blur_conditional.blur_options",
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250 "size": $input_data.blur_conditional.kernel_size
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251 }
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252 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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253 ,
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254 #end if
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255 #end if
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256 #if $input_data.downsample_conditional.downsample_select == "Yes":
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257 {
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258 "name": "downsample",
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259 "parameters": {
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260 "scale": "$input_data.downsample_conditional.scale"
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261 }
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262 }
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263 #end if
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264 ]
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265 }
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266 #end if
0
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267 ],
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268 "segmentation_parameters": {
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269 #if $task.segmentation_parameters.nuclear_channel != "None":
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270 "nuclear_channel": "$task.segmentation_parameters.nuclear_channel",
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271 #else:
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272 "nuclear_channel": null,
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273 #end if
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274 #if $task.segmentation_parameters.entity_fill_channel != "None":
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275 "entity_fill_channel": "$task.segmentation_parameters.entity_fill_channel",
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276 #else:
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277 "entity_fill_channel": null,
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278 #end if
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279 "diameter": $task.segmentation_parameters.diameter,
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280 "flow_threshold": $task.segmentation_parameters.flow_threshold,
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281 "cellprob_threshold": $task.segmentation_parameters.cellprob_threshold,
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282 "minimum_mask_size": $task.segmentation_parameters.minimum_mask_size
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283 },
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284 "polygon_parameters": {
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285 "simplification_tol": $task.polygon_parameters.simplification_tol,
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286 "smoothing_radius": $task.polygon_parameters.smoothing_radius,
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287 "minimum_final_area": $task.polygon_parameters.minimum_final_area
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288 }
1
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289 }#if $i != $task_n
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290 ,
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291 #end if
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292 #end for
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293 ],
0
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294 "segmentation_task_fusion": {
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295 "entity_fusion_strategy": "$segmentation_task_fusion.entity_fusion_strategy",
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296 "fused_polygon_postprocessing_parameters": {
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297 "min_distance_between_entities": $segmentation_task_fusion.min_distance_between_entities,
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298 "min_final_area": $segmentation_task_fusion.min_final_area
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299 }
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300 },
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301 "output_files": [
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302 {
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303 #if $vpt_config.output_files.entity_types_output != "both":
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304 "entity_types_output": ["$vpt_config.output_files.entity_types_output"],
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305 #else:
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306 "entity_types_output": [
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307 "nuclei",
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308 "cell"
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309 ],
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310 #end if
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311 "files": {
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312 "run_on_tile_dir": "result_tiles/",
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313 "mosaic_geometry_file": "cellpose2_mosaic_space.parquet",
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314 "micron_geometry_file": "cellpose2_micron_space.parquet",
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315 "cell_metadata_file": "cellpose2_cell_metadata.csv"
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316 }
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317 }
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318 ]
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319 }
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320 ]]></configfile>
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321 </configfiles>
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322 <inputs>
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323 <expand macro="common_input"/>
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324 <param argument="--detected_transcripts" type="data" format="csv" label="Detected transcripts"/>
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325 <param argument="--tile_size" type="integer" min="1" value="4096" label="Number of pixels for the width and height of each tile"/>
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326 <param argument="--tile_overlap" type="integer" min="0" max="100" value="10" label="Overlap between adjacent tiles (%)" help="Default: 10% of tile size"/>
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327 <param argument="--max_row_group_size" type="integer" min="1000" value="" optional="true" label="Maximum number of rows in row groups inside output parquet files"/>
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328 <section name="vpt_config" title="Segmentation configuration file">
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329 <section name="experiment_properties" title="Experiment properties" help="Specify the z-indexes and z-positions in the data. It is used to apply 2D segmentation to 3D data and calculate distances on the z-axis.">
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330 <param argument="--z_positions_um" type="text" value="1.5, 3, 4.5, 6, 7.5, 9, 10.5" label="Z-layer positions in micron">
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331 <expand macro="sanitize_digits"/>
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332 </param>
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333 </section>
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334 <section name="segmentation_tasks" title="Segmentation tasks" help="A list of segmentation tasks to perform sequentially. The VPT only supports 9 tasks in a single segmentation algorithm. If more tasks are needed, users are encouraged to run vpt multiple times and combine the segmentation outputs post hoc.">
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335 <repeat name="segmentation_task" min="1" max="9" title="Segmentation tasks">
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336 <param argument="--entity_types_detected" type="select" label="Detect cell or nucleus?">
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337 <option value="cell">cell</option>
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338 <option value="nucleus">nucleus</option>
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339 <option value="both">both</option>
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340 </param>
1
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341 <param argument="--z_layers" type="text" value="3" optional="false" label="Comma-separated list of z-index images to segment.">
0
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342 <expand macro="sanitize_digits"/>
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343 </param>
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344 <section name="segmentation_properties" title="Segmentation properties">
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345 <param argument="--model" type="select" label="Cellpose model">
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346 <option value="cyto2">cyto2</option>
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347 <option value="nuclei">nuclei</option>
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348 <option value="null">null</option>
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349 </param>
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350 <param argument="--model_dimensions" type="select" label="Model dimensions" help="2D applies the 2D Cellpose model to all z-planes specified in the z_layers list separately and the results are combined into a 3D output. 3D applies the native-3D Cellpose model to all z-planes specified in the z_layers list.">
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351 <option value="2D">2D</option>
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352 <option value="3D">3D</option>
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353 </param>
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354 <param argument="--custom_weights" type="data" format="data" optional="true" label="Custom Cellpose weights file"/>
2
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355 <section name="channel_map" title="Channel map" expanded="true" help="Specify the channel map for the segmentation task with the corresponding task input data">
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356 <conditional name="channel_red_conditional">
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357 <param name="red" type="select" label="The stain that will be used for red channel">
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358 <expand macro="channel_options_none"/>
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359 </param>
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360 <expand macro="channel_map_conditional_childs"/>
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361 </conditional>
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362 <conditional name="channel_green_conditional">
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363 <param name="green" type="select" label="The stain that will be used for green channel">
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364 <expand macro="channel_options_none"/>
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365 </param>
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366 <expand macro="channel_map_conditional_childs"/>
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367 </conditional>
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368 <conditional name="channel_blue_conditional">
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369 <param name="blue" type="select" label="The stain that will be used for blue channel">
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370 <expand macro="channel_options_none"/>
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371 </param>
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372 <expand macro="channel_map_conditional_childs"/>
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373 </conditional>
0
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374 </section>
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375 </section>
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376 <section name="segmentation_parameters" title="Segmentation parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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377 <param name="nuclear_channel" type="select" label="Nuclear channel">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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378 <expand macro="channel_options_none">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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379 <option value="all">all</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
380 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
381 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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382 <param name="entity_fill_channel" type="select" label="Entity fill channel">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
383 <expand macro="channel_options_none">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
384 <option value="all">all</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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385 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
386 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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387 <param name="diameter" type="integer" min="0" value="30" label="Diameter" help="A default value of 0 automatically estimate the diameter with Cellpose. Too small diameter leads to fragmented cells and too big one leads to over-merged cells"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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388 <param name="flow_threshold" type="float" min="0" max="1" value="0.4" label="Flow threshold" help="Maximum allowed error of the flows for each mask. Increase if cellpose is not returning as many ROIs as you’d expect, and decrease if cellpose is returning too many ill-shaped ROIs"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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389 <param name="cellprob_threshold" type="float" min="-6" max="6" value="0.0" label="Cellprobe threshold" help="Decrease this threshold if cellpose is not returning as many ROIs as you’d expect. Similarly, increase this threshold if cellpose is returning too ROIs particularly from dim areas."/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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390 <param name="minimum_mask_size" type="integer" min="-1" value="15" label="Minimum number of pixels per mask" help="This can be turned off with -1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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391 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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392 <section name="polygon_parameters" title="Polygon parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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393 <param name="simplification_tol" type="integer" min="0" value="2" label="Simplification tolerance" help="The acceptable loss of precision when simplifying cell boundaries. Even a small amount of simplification (2 px) dramatically improves processing time" />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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394 <param name="smoothing_radius" type="integer" min="0" value="10" label="Smoothing radius" help="The size of a smoothing operation comparable to morphologically closing and then opening the cell mask using the same structuring element" />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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395 <param name="minimum_final_area" type="integer" min="0" value="500" label="Minimum final area" help="Minimum area of a polygon to retain the cell. Used to filter spurious detections." />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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396 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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397 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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398 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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399 <section name="segmentation_task_fusion" title="Segmentation task fusion" help="Specify how the geometries produced by each segmentation task should be combined">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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400 <param name="entity_fusion_strategy" type="select" label="Entity fusion strategy">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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401 <option value="harmonize" selected="true">harmonize (recommended)</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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402 <option value="union">union</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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403 <option value="larger">larger</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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404 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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405 <param name="min_distance_between_entities" type="integer" min="0" value="2" label="Minimum distance between entities" help="When polygons are subtracted from one another, the space between the cells is zero. In order to provide some separation between cells, a minimum distance between these cell can be specified."/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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406 <param name="min_final_area" type="integer" min="0" value="0" label="Minimum area" help="After polygon subtraction, cells smaller than this threshold will be removed"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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407 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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408 <section name="output_files" title="Output files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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409 <param name="entity_types_output" type="select" label="Output entity types">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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410 <option value="cell">cell</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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411 <option value="nucleus">nucleus</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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412 <option value="both">both</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
413 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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414 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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415 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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416 <section name="qc_params" title="QC metrics parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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417 <param argument="--experiment-name" type="text" value="Analysis Timestamp" label="The name of the experiment to be used as the index in the output csv and segmentation report">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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418 <sanitizer invalid_char="">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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419 <valid initial="string.letters,string.digits">
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420 <add value="_" />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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421 </valid>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
422 </sanitizer>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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423 <validator type="regex">[0-9a-zA-Z_]+</validator>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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424 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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425 <param argument="--input-z-index" type="integer" min="0" value="2" label="The Z plane of the mosaic tiff images to use for the patch"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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426 <param argument="--transcript-count-filter-threshold" type="integer" min="0" value="100" label="The cell transcript count threshold used for computing metrics and clustering"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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427 <param argument="--volume-filter-threshold" type="integer" min="0" value="200" label="The cell volume threshold used for computing metrics and clustering"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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428 <param argument="--red-stain-name" type="select" label="The stain that will be used for red channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
429 <expand macro="channel_options_none"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
430 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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431 <param argument="--green-stain-name" type="select" label="The stain that will be used for green channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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432 <expand macro="channel_options_basic">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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433 <option value="None">None</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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434 <option value="DAPI">DAPI</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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435 <option value="PolyT" selected="true">PolyT</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
436 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
437 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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438 <param argument="--blue-stain-name" type="select" label="The stain that will be used for blue channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
439 <expand macro="channel_options_basic">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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440 <option value="None">None</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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441 <option value="DAPI" selected="true">DAPI</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
442 <option value="PolyT">PolyT</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
443 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
444 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
445 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
446 <expand macro="advanced_output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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447 </inputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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448 <outputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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449 <collection name="vpt_results" type="list" label="${tool.name} on ${on_string}: VPT Results">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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450 <discover_datasets pattern="(?P&lt;name&gt;.+)\.csv$" format="csv" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
451 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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452 <collection name="vpt_boundaries" type="list" label="${tool.name} on ${on_string}: VPT segmentation boundaries">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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453 <discover_datasets pattern="(?P&lt;name&gt;.+)\.parquet$" format="parquet" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
454 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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455 <data name="vpt_qc" format="html" from_work_dir="output/metrics.html" label="${tool.name} on ${on_string}: VPT QC"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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456 <collection name="vpt_config_out" type="list" label="${tool.name} on ${on_string}: VPT Config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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457 <discover_datasets pattern="(?P&lt;name&gt;.+)\.json$" format="json" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
458 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
459 <expand macro="common_output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
460 </outputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
461 <tests>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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462 <!-- test 1: one segmentation task -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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463 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
464 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
465 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
466 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
467 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
468 <section name="experiment_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
469 <param name="z_positions_um" value="1.5, 3, 4.5, 6, 7.5, 9, 10.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
470 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
471 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
472 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
473 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
474 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
475 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
476 <param name="model" value="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
477 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
478 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
479 <conditional name="channel_red_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
480 <param name="red" value="Cellbound1"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
481 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
482 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
483 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
484 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
485 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
486 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
487 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
488 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
489 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
490 <conditional name="channel_green_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
491 <param name="green" value="Cellbound3"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
492 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
493 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
494 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
495 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
496 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
497 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
498 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
499 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
500 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
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501 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
502 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
503 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
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504 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
505 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
506 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
507 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
508 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
509 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
510 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
511 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
512 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
513 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
514 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
515 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
516 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
517 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
518 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
519 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
520 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
521 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
522 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
523 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
524 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
525 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
526 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
527 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
528 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
529 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
530 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
531 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
532 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
533 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
534 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
535 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
536 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
537 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
538 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
539 <param name="experiment_name" value="cyto2_1task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
540 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
541 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
542 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
543 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
544 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
545 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
546 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
547 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
548 <has_text_matching expression="0,2,0,3,0,0,0,0,2,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
549 <has_text_matching expression="3,6,3,2,1,3,3,1,3,16,0,8,113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
550 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
551 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
552 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
553 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
554 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
555 <has_text_matching expression=",752.854533232[0-9]+,315.600965641[0-9]+,5.50107977386[0-9]+,310.1669732237[0-9]+,"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
556 <has_text_matching expression=",416.540438981[0-9]+,68.7110642977[0-9]+,9.67291568732[0-9]+,64.4947481953[0-9]+,"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
557 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
558 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
559 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
560 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
561 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
562 <has_text_matching expression="86,10,285.00012,10.13364,0.0,816.0,153.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
563 <has_text_matching expression="229,10,274.95612,35.72964,0.0,723.0,390.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
564 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
565 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
566 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
567 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
568 <has_text_matching expression=",Cell count,Cell volume"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
569 <has_text_matching expression="All cells,814,1572.4,1533.3,735.8,654.0,92.1,108.0,96.4,68.2,0.0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
570 <has_text_matching expression="Cells after filtering,700,1694.1,1667.9,851.1,810.5,104.5,111.0,95.9,63.2,0.06"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
571 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
572 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
573 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
574 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
575 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
576 <has_text_matching expression="813229843.0,4955524.23422[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
577 <has_text_matching expression="587668405.0,22623235.0759[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
578 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
579 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
580 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
581 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
582 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
583 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
584 <has_size size="232259" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
585 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
586 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
587 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
588 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
589 <has_size size="215395" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
590 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
591 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
592 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
593 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
594 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
595 <has_text text="VPT Segmentation Report (cyto2_1task)"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
596 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;814&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
597 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;654.0&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
598 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
599 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
600 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
601 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
602 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
603 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
604 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
605 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
606 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
607 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
608 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
609 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
610 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
611 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
612 <has_text_matching expression="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
613 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
614 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
615 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
616 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
617 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
618 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
619 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
620 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
621 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
622 <has_text_matching expression="Sum signals finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
623 <has_text_matching expression="Generate segmentation metrics finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
624 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
625 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
626 </test>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
627 <!-- test 2: two segmentation tasks -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
628 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
629 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
630 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
631 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
632 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
633 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
634 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
635 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
636 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
637 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
638 <param name="model" value="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
639 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
640 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
641 <conditional name="channel_red_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
642 <param name="red" value="Cellbound1"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
643 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
644 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
645 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
646 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
647 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
648 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
649 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
650 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
651 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
652 <conditional name="channel_green_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
653 <param name="green" value="Cellbound3"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
654 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
655 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
656 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
657 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
658 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
659 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
660 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
661 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
662 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
663 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
664 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
665 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
666 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
667 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
668 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
669 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
670 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
671 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
672 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
673 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
674 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
675 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
676 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
677 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
678 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
679 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
680 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
681 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
682 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
683 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
684 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
685 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
686 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
687 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
688 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
689 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
690 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
691 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
692 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
693 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
694 <param name="model" value="nuclei"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
695 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
696 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
697 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
698 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
699 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
700 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
701 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
702 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
703 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
704 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
705 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
706 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
707 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
708 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
709 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
710 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
711 <param name="nuclear_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
712 <param name="entity_fill_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
713 <param name="diameter" value="55"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
714 <param name="flow_threshold" value="0.8"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
715 <param name="cellprob_threshold" value="-3.0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
716 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
717 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
718 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
719 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
720 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
721 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
722 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
723 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
724 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
725 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
726 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
727 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
728 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
729 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
730 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
731 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
732 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
733 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
734 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
735 <param name="experiment_name" value="cyto2_2task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
736 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
737 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
738 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
739 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
740 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
741 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
742 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
743 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
744 <has_text_matching expression="0,0,0,0,0,0,0,0,0,1,0,1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
745 <has_text_matching expression="1,2,0,1,2,1,3,0,3,8,0,4,18,2,1,2,2,0,0,2,1,0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
746 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
747 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
748 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
749 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
750 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
751 <has_text_matching expression=",833.754893427[0-9]+,340.820612890[0-9]+,1.070367649097[0-9]+,334.8351650026[0-9]+,-3.129014413402[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
752 <has_text_matching expression=",879.995798798[0-9]+,357.422829969[0-9]+,2.811753148503[0-9]+,352.3315077075[0-9]+,-2.496679594480[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
753 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
754 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
755 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
756 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
757 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
758 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
759 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
760 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
761 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
762 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
763 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
764 <has_text_matching expression=",Cell count,Cell volume"/>
1
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
765 <has_text_matching expression="All cells,811,1588.0,1549.9,740.5,669.0,92.2,109.0,96.7,68.6,0.0"/>
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
766 <has_text_matching expression="Cells after filtering,698,1711.6,1705.9,856.1,817.5,104.6,111.0,96.2,63.7,0.06"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
767 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
768 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
769 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
770 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
771 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
772 <has_text_matching expression="56353541.0,781480.649952[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
773 <has_text_matching expression="53118509.0,808077.377016[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
774 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
775 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
776 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
777 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
778 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
779 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
780 <has_size size="232259" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
781 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
782 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
783 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
784 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
785 <has_size size="215395" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
786 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
787 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
788 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
789 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
790 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
791 <has_text text="VPT Segmentation Report (cyto2_2task)"/>
1
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
792 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;811&lt;/b&gt;&lt;/p&gt;"/>
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
793 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;669.0&lt;/b&gt;&lt;/p&gt;"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
794 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
795 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
796 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
797 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
798 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
799 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
800 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
801 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
802 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
803 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
804 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
805 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
806 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
807 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
808 <has_text_matching expression="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
809 <has_text_matching expression="nuclei"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
810 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
811 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
812 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
813 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
814 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
815 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
816 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
817 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
818 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
819 <has_text_matching expression="Sum signals finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
820 <has_text_matching expression="Generate segmentation metrics finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
821 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
822 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
823 </test>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
824 <!-- test 3: one segmentation task with custom weight -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
825 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
826 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
827 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
828 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
829 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
830 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
831 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
832 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
833 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
834 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
835 <param name="model" value="null"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
836 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
837 <param name="custom_weights" location="https://zenodo.org/records/15319018/files/CP_20230830_093420"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
838 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
839 <conditional name="channel_red_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
840 <param name="red" value="Cellbound1"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
841 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
842 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
843 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
844 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
845 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
846 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
847 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
848 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
849 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
850 <conditional name="channel_green_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
851 <param name="green" value="Cellbound3"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
852 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
853 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
854 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
855 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
856 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
857 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
858 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
859 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
860 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
861 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
862 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
863 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
864 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
865 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
866 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
867 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
868 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
869 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
870 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
871 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
872 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
873 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
874 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
875 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
876 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
877 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
878 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
879 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
880 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
881 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
882 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
883 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
884 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
885 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
886 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
887 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
888 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
889 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
890 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
891 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
892 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
893 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
894 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
895 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
896 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
897 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
898 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
899 <param name="experiment_name" value="custom_1task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
900 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
901 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
902 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
903 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
904 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
905 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
906 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
907 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
908 <has_text_matching expression="6,11,4,0,5,2,1,0,1,2,1,2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
909 <has_text_matching expression="0,1,0,0,0,0,1,0,0,4"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
910 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
911 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
912 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
913 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
914 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
915 <has_text_matching expression="168.0683921161[0-9]+,246.3592447472[0-9]+,-1.507707574380[0-9]+,243.9322371166[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
916 <has_text_matching expression="1540.721726928[0-9]+,412.175889439[0-9]+,2.951632912099[0-9]+,404.3500198495[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
917 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
918 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
919 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
920 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
921 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
922 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
923 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
924 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
925 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
926 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
927 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
928 <has_text_matching expression=",Cell count,Cell volume"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
929 <has_text_matching expression="All cells,93[0-9]+,121\d*(\.\d+)?,118\d*(\.\d+)?,60\d*(\.\d+)?,49\d*(\.\d+)?,7\d*(\.\d+)?,10\d*(\.\d+)?,9\d*(\.\d+)?,6\d*(\.\d+)?,0.0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
930 <has_text_matching expression="Cells after filtering,659,1532.9,1553.5,850.2,837.0,104.8,112.0,90.2,53.8,0.15"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
931 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
932 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
933 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
934 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
935 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
936 <has_text_matching expression="73446567.0,1605103.666715[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
937 <has_text_matching expression="1642190888.0,16154095.44810[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
938 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
939 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
940 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
941 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
942 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
943 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
944 <has_size size="375308" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
945 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
946 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
947 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
948 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
949 <has_size size="365132" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
950 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
951 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
952 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
953 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
954 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
955 <has_text text="VPT Segmentation Report (custom_1task)"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
956 <has_text_matching expression="Cell count: &lt;b class=&quot;summary__value&quot;&gt;93[0-9]+&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
957 <has_text_matching expression="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;49\d*(\.\d+)?&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
958 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
959 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
960 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
961 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
962 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
963 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
964 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
965 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
966 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
967 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
968 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
969 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
970 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
971 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
972 <has_text_matching expression="null"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
973 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
974 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
975 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
976 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
977 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
978 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
979 <assert_contents>
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980 <has_text_matching expression="run_segmentation finished"/>
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981 <has_text_matching expression="Partition transcripts finished"/>
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982 <has_text_matching expression="Sum signals finished"/>
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983 <has_text_matching expression="Generate segmentation metrics finished"/>
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984 </assert_contents>
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985 </output>
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986 </test>
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987 </tests>
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988 <help>
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989 The Vizgen Post-processing Tool (VPT) is a scalable and reproducible tool which enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
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990
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991 The **Vizgen Post-processing Tool - Segment Cells** performes **run_segmentation**, **partition_transcripts**, **sum_signals**, **derive-entity-metadata**, and **generate-segmentation-metrics** of the VPT pipeline. The segmentation
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992
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993 Segmentation parameters for CellPose can be assigned with "**Segmentation configuration file**".
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994
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995 The segmentation parameters describes a series of steps to perform on the input data. Using the same segmentation algorithm on a series of experiments ensures that they are processed identically and reproducibly.
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996
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997 The segmentation parameters has 3 main sections:
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998
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999 1. **Experiment properties**:
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1000 - Holds descriptions of the way the data was collected. Specifically, it must contain a list of the z-indexes and z-positions in the data. This data is used to apply 2D segmentation to 3D data and calculate distances on the z-axis.
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1001 2. **Segmentation tasks**:
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1002 - Holds a list of segmentation tasks to perform. These tasks will be performed sequentially. By running different segmentation tools in "tasks" and combining their output, it is possible to improve cell detection. For example, combining the results of CellPose with the `cyto2` model and the `nuclei` model can dramatically improve the segmentation F1 score over either method alone.
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1003 3. **Segmentation task fusion**:
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1004 - Specifies how the geometries produced by each segmentation task should be combined. All `segmentation_task_fusion` options will produce a non-overlapping set of valid geometries.
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1005 4. **Output files**:
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1006 - Specifies which entity types should be written to disk in the output folder and the file names they should receive.
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1007
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1008
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1009 For more information on the VPT pipeline, please refer to the `VPT user guide`_
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1010
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1011 -----
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1012
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1013 If you want to use a custom-trained model, set the CellPose model to null and provide the custom weights file.
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1014
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1015
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1016 .. class:: infomark
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1017
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1018 **Note:** VPT only supports **9** tasks in a single segmentation algorithm. If more tasks are needed, users are encouraged to run vpt multiple times and combine the segmentation outputs post hoc.
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1019
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1020 .. class:: infomark
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1021
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1022 **Note:** VPT tool on Galaxy only uses **CellPose** algorithm for cell segmentation.
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1023
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1024 .. _`VPT user guide`: https://vizgen.github.io/vizgen-postprocessing/
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1025 </help>
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1026 <expand macro="citations" />
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1027 </tool>